Hijacking SARS-CoV-2/ACE2 Receptor Interaction by Natural and Semi-synthetic Steroidal Agents Acting on Functional Pockets on the Receptor Binding Domain

Abstract

The coronavirus disease 2019 (COVID-19) is a respiratory tract infection caused by the severe acute respiratory syndrome coronavirus (SARS)-CoV-2. In light of the urgent need to identify novel approaches to be used in the emergency phase, we have embarked on an exploratory campaign aimed at repurposing natural substances and clinically available drugs as potential anti-SARS-CoV2-2 agents by targeting viral proteins. Here we report on a strategy based on the virtual screening of druggable pockets located in the central β-sheet core of the SARS-CoV-2 Spike's protein receptor binding domain (RBD). By combining an in silico approach and molecular in vitro testing we have been able to identify several triterpenoid/steroidal agents that inhibit interaction of the Spike RBD with the carboxypeptidase domain of the Angiotensin Converting Enzyme (ACE2). In detail, we provide evidence that potential binding sites exist in the RBD of the SARS CoV-2 Spike protein and that occupancy of these pockets reduces the ability of the RBD to bind to the ACE2 consensus in vitro. Naturally occurring and clinically available triterpenoids such as glycyrrhetinic and oleanolic acids, as well as primary and secondary bile acids and their amidated derivatives such as glyco-ursodeoxycholic acid and semi-synthetic derivatives such as obeticholic acid reduces the RBD/ACE2 binding. In aggregate, these results might help to define novel approaches to COVID-19 based on SARS-CoV-2 entry inhibitors.

In Silico Drug Repositioning Against Human NRP1 to Block SARS-CoV-2 Host Entry

“…Several in silico and in vivo drug repurposing studies are carried out using proteases (3CL pro and PL pro ) and RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 as targets (Bharadwaj et al, 2020;Ghosh et al, 2020;Gul et al, 2020;Li et al, 2020c;Wang, 2020). In addition, host proteins TMPRSS2 and ACE2 which primes protein S and mediates SARS-CoV-2 entry to host, respectively, are targeted for drug repositioning as well (Bagheri and Niavarani, 2020;Busnadiego et al, 2020;Carino et al, 2020;Choudhary et al, 2020;Durdagi, 2020;Kumar et al, 2020;Singh et al, 2020b).…”

“…So, medication is still an essential element to combat COVID-19. Vital enzymes of SARS-CoV-2 such as proteases (3CL pro and M pro ) and RNA polymerase (RdRp), or virus binding receptors on the host such as ACE2 or TMPRSS2 are generally targeted in drug repurposing studies (Bagheri and Niavarani, 2020;Busnadiego et al, 2020;Carino et al, 2020;Gul et al, 2020;Kumar et al, 2020;Li et al, 2020c;Singh et al, 2020b). Recent studies reported protein S binds to NRP1 which facilitates SARS-CoV-2 host entry (Cantuti-Castelvetri et al, 2020;Daly et al, 2020).…”

Current Updates on Naturally Occurring Compounds Recognizing SARS-CoV-2 Druggable Targets

“…In contrast, glyco-ursodeoxycholic acid (Figure 16c), chenodeoxycholic acid (Figure 16a), and glyco-chenodeoxycholic acid (Figure 16d) reduce the Spike binding to the ACE2 receptor by at least 20% in a concentration-dependent manner. Despite these promising in-vitro results, the studies have several limitations; e.g., the effects of these natural molecules were not tested on viral replication [122]. The experimental results found that the incubation of the Spike-ACE2 complex with these naturally occurring triterpenoids reduced the Spike-ACE2 binding in a concentrationdependent way.…”

“…In contrast, glyco-ursodeoxycholic acid (Figure 16c), chenodeoxycholic acid (Figure 16a), and glyco-chenodeoxycholic acid (Figure 16d) reduce the Spike binding to the ACE2 receptor by at least 20% in a concentrationdependent manner. Despite these promising in-vitro results, the studies have several limitations; e.g., the effects of these natural molecules were not tested on viral replication [122]. scaffold of the ursodeoxycholic acid (Figure 16b) is surrounded by Lys378, Thr376, Phe377, Tyr380, and Pro384 and formed a hydrogen bond with Cys379 [122].…”

“…Despite these promising in-vitro results, the studies have several limitations; e.g., the effects of these natural molecules were not tested on viral replication [122]. scaffold of the ursodeoxycholic acid (Figure 16b) is surrounded by Lys378, Thr376, Phe377, Tyr380, and Pro384 and formed a hydrogen bond with Cys379 [122]. The in vitro screening confirmed that the ursodeoxycholic acid and its taurine conjugate exerted a limited inhibitory activity towards Spike-ACE2 complex.…”